Data collection and refinement statistics.

<p>*Data for highest resolution shell are given in the parenthesis.</p

Comparison of conformation of catalytic aspartates in the structures at pH 2.0 and pH7.0.

<p>Comparison of conformation of catalytic aspartates in the structures at pH 2.0 and pH7.0.</p

Structural comparison of present complex with tetrahedral intermediate complex [21] and product peptide complex [22]:

<p>Stereo diagram showing the ligand atoms at the catalytic centre along with catalytic aspartates. Protein Cα atoms are used in the structural superposition. WAT1 is within 1 Å from an oxygen atom in the newly generated gem-diol <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007860#pone.0007860-Kumar1" target="_blank">[21]</a> or carboxyl group <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007860#pone.0007860-Das1" target="_blank">[22]</a>.</p

Fit of carboxy terminal product peptide and active site water molecules into 2Fo-Fc electron density.

<p>The electron density map is contoured at 1.0σ level. The carboxyl product peptide ( violetpurple) and the active site water molecules are shown in the two orientations.</p

Relative positions of WAT1 and the modelled substrate in the active site:

<p>Diagram showing superposition of three structures: 1) present structure (yellow carbon), 2) unliganded HIV-1 protease (magenta carbon, PDB Id 1LV1) and 3) inactive HIV-1 protease/substrate complex (green carbon, PDB Id 1KJH). Water molecule observed in unliganded HIV-1 protease is also shown (magenta). The distances to the scissile carbon atom are indicated. SA OMIT density contoured at 3σ level is also shown for WAT1.</p

Comparison of interactions of catalytic aspartates in the structures at pH 2.0 and pH7.0.

<p>Comparison of interactions of catalytic aspartates in the structures at pH 2.0 and pH7.0.</p